Polymerase Structure Alignments - v4 Update (July 2022)

<p>v4&nbsp;update (July 2022) of superposed viral polymerase structures using the methodology described in&nbsp;<br> <em>A Comprehensive Superposition of Viral Polymerase Structures</em>&nbsp;by Olve Peersen, <a href="https://www.mdpi.com/1999-4915/11/8/745">Viruses 2019 11(8) 745</a>.</p> <p>&nbsp; &bull; &nbsp;<strong>_All_PDBs_v4.zip</strong> contains a single directory with coordinate files for 917 structures taken from 628 PDB entries. &nbsp;Uncompressed size is 1.6&nbsp;GB.</p> <p>&nbsp; &bull; <strong>Polymerases_v4.zip</strong> contains the complete set of files from the superpositions, including the _All_PDBs/ directory. &nbsp; Uncompressed size is 5.7&nbsp;GB.</p> <p>---------------------------------------------------------------------------------------------------------------<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; POLYMERASE STRUCTURES community page at Zenodo.org&nbsp;</p> <p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;v4 Release &nbsp;July 19, 2022</p> <p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 917 structures from 628 PDB entries</p> <p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; http://www.zenodo.org/communities/pols/&nbsp;<br> =========================================================================================</p> <p>This directory contains a large collection viral polymerase structure coordinates that&nbsp;have been superposed using the methods described in Peersen, Viruses 2019, 11(8), 745.&nbsp;</p> <p>They are released into the public domain under the Creative Commons Attribution (CC BY)&nbsp;license. &nbsp;</p> <p>Please cite the following two references for any derivative work:</p> <p>&nbsp; &nbsp;1) Reference to the publication describing the methodology:<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Peersen, OB<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; A Comprehensive Superposition of Viral Polymerase Structures.<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Viruses 2019, 11(8), 745 &nbsp;&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; https://doi.org/10.3390/v11080745</p> <p>&nbsp; &nbsp;2) DOI reference that always resolves to the latest release of the dataset:<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Peersen, OB<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Polymerase Structure Alignments<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; https://doi.org/10.5281/zenodo.3361874</p> <p><br> ---------------------------------------------------------------------------------------------<br> Olve Peersen &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Olve.Peersen@ColoState.edu<br> Professor<br> Biochemistry &amp; Molecular Biology<br> 1870 Campus Delivery<br> Colorado State University<br> Ft. Collins, CO &nbsp;80523-1870<br> -------------------------------------------------------------------------</p> <p>=============================================================================</p> <p>v4&nbsp;&nbsp; &nbsp;220719 - Many updates and several news sets, as outlined below.&nbsp;<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; The total count is now 917 polymerase structures from 628 PDB entries</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;2-rddp: Foamyvirus FOAM added, but rest of set left unchanged</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;3-dsdn: Simplified as hsv1 was pulled into its own set (see below)</p> <p><br> &nbsp;&nbsp; &nbsp;NEW&nbsp;&nbsp; &nbsp;alph: Alphaviruses - &nbsp;&nbsp; &nbsp; RRV: 7f0s,<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;SINV: 7vb4, 7vw5</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;aren:&nbsp;&nbsp; &nbsp;Lassa:&nbsp;&nbsp; &nbsp;7ckl, 7ela, 7och, 7oe3, 7oe7, 7oea, 7oeb,<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;7ojj, 7ojk, 70jl, 7ojn<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Machupo: 7ckm, 7el9, 7elb, 7elc, 7vgq, 7vh1, 7vh2, 7vh3</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;buny:&nbsp;&nbsp; &nbsp;RVF: &nbsp; 7eei<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;LaCrosse: 7ori, 7orj, 7ork, 7orl, 7orm, 7orn, 7oro</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;coro: &nbsp;&nbsp; &nbsp;7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7krn, 7kro, 7krp,&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm&nbsp;</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;fluv:&nbsp;&nbsp; &nbsp;7nha, 7nhc, 7nhx, 7ni0, 7nik, 7nil, 7nir, 7nis, 7nj3, 7nj4, 7nj5,&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;&nbsp;7nj7, 7nk1, 7nk2, 7nk4, 7nk6, 7nk8, 7nka, 7nkc, 7nki, 7nkr, 7z42,&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;7z43, 7z43, 7z4o, 7z4o</p> <p>&nbsp;&nbsp; &nbsp;NEW&nbsp;&nbsp; &nbsp;foam: Foamyviruses - 7o0g, 7o0h, 7024<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Created FOAM.pdb from core of 7o0g.pdb, which was&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;superposed on rddp set, but the orientations of other&nbsp;<br> &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;members of that set (HIV,MMLV,TERT) were not updated.</p> <p>&nbsp;&nbsp; &nbsp;NEW&nbsp;&nbsp; &nbsp;hsv1: Herpes Simplex Virus - 2gv9, 7luf</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;pest: Classic Swine Fever Virus: 7ekj</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;poxv: 7amv, 7aof, 7aoh, 7aoz, 7ap8, 7ap9</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;rb69: 2atq, 7f4y</p> <p>&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;tavp: 7om2, 7om6, 7om7, 7om9, 7oma<br> &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;</p>